It is possible that contaminants from the steel have worked their way through the coatings during the cure cycle causing blemishes. If the steel has been properly cleaned prior to plating, this probably isn't the culprit.
You ask if it could be the zinc. Blistering during the cure cycle can occur if the plating's film build is too high. You can run test panels or parts through your system with various film thicknesses of zinc plating and powder coat as you would normally. This will illustrate how a higher zinc film build vs. a lower zinc film build reacts during the cure cycle. Generally, a lower film build of zinc is preferred. It would be a good idea to check with your plating supplier for their recommendations.